Updated formatting on website

.Rbuildignore

@@ -11,6 +11,8 @@
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^README\.Rmd$
+^README\.qmd$
 ^tools$
 ^scratch.R$
 ^altdoc$
+^_quarto$

.gitignore

@@ -14,3 +14,4 @@ inst/doc
 scratch*
 *.psd
 altdoc/freeze.rds
+^_quarto$

README.md

@@ -1,27 +1,52 @@
-
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 # handwriter
 
+
 <!-- badges: start -->
 <!-- badges: end -->
 
-The handwriter package performs writership analysis of a handwritten
-*questioned document* where the questioned document was written by one
-of *closed-set* of potential writers. For example, a handwritten bomb
-threat is found in a science classroom, and the police are able to
-determine that the note could only have been written by one of the
-students in 4th period science. The handwriter package builds a
-statistical model to estimate a *writer profile* from known handwriting
-samples from each writer in the closed-set. A writer profile is also
-estimated from the questioned document. The statistical model compares
-the writer profile from the questioned document with each of the writer
-profiles from the closed-set of potential writers and estimates the
-posterior probability that each closed-set writer wrote the questioned
-document.
-
-## Installation
+Handwriter is designed to assist forensic examiners by analyzing
+handwritten documents against a *closed set* of potential writers. It
+determines the probability that each writer wrote the document. Whether
+you are a forensic document examiner, legal professional, academic, or
+simply curious about how statistics are applied to handwriting,
+handwriter provides an automated way to evaluate handwriting samples.
+
+## Quick Start
+
+### VIEW A DEMO
+
+View a demo of handwriter on handwritten documents from the CSAFE
+Handwriting Database. Go to
+[demo](https://csafe.shinyapps.io/handwriterAppDemo/).
+
+### SIMULATE CASEWORK WITH EXAMPLE DOCUMENTS
+
+#### INSTALLATION
+
+Handwriter requires R, RStudio IDE, and JAGS.
+
+-   Install R and RStudio from
+    [POSIT](https://posit.co/download/rstudio-desktop/)
+-   Install JAGS from
+    [SourceForge](https://sourceforge.net/projects/mcmc-jags/files/)
+
+#### LAUNCH THE APP
+
+Open RStudio, navigate to the console window, and type:
+
+``` r
+install.packages("devtools")
+devtools::install_github("CSAFE-ISU/handwriterApp")
+library(handwriterApp)
+handwriterApp()
+```
+
+In the pop-up window, click **Open in Browser**. If you use the app in
+the pop-up window instead of in a browser, some links will not work.
+
+Click **Simulate Casework** and follow the instructions in the app.
+
+## Advanced
 
 You can install handwriter from CRAN with:
 
@@ -195,7 +220,7 @@ template_data <- format_template_data(template = template)
 plot_cluster_fill_counts(template_data, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png"
+<img src="man/figures/README-unnamed-chunk-5-1.png"
 style="width:100.0%" />
 
 ### STEP 3: Fit a Hierarchical Model
@@ -260,7 +285,7 @@ but the model data is already in the correct format.)
 plot_cluster_fill_counts(formatted_data=model, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-7-1.png"
+<img src="man/figures/README-unnamed-chunk-8-1.png"
 style="width:100.0%" />
 
 The bars across the top of each graph show the Writer ID. Each graph has
@@ -301,7 +326,7 @@ View a trace plot of a variable.
 plot_trace(variable = "mu[1,1]", model = model)
 ```
 
-<img src="man/figures/README-unnamed-chunk-10-1.png"
+<img src="man/figures/README-unnamed-chunk-11-1.png"
 style="width:100.0%" />
 
 If we need to, we can drop the beginning MCMC iterations for burn-in.
@@ -373,7 +398,7 @@ the cluster fill counts observed in each questioned document.
 plot_cluster_fill_counts(analysis, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-15-1.png"
+<img src="man/figures/README-unnamed-chunk-16-1.png"
 style="width:100.0%" />
 
 View the posterior probabilities of writership.

README.Rmd → README.qmd

@@ -1,9 +1,9 @@
 ---
-output: github_document
+title: "handwriter"
+format: html
+editor: visual
 ---
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -13,14 +13,43 @@ knitr::opts_chunk$set(
 )
 ```
 
-# handwriter
-
 <!-- badges: start -->
 <!-- badges: end -->
 
-The handwriter package performs writership analysis of a handwritten *questioned document* where the questioned document was written by one of *closed-set* of potential writers. For example, a handwritten bomb threat is found in a science classroom, and the police are able to determine that the note could only have been written by one of the students in 4th period science. The handwriter package builds a statistical model to estimate a *writer profile* from known handwriting samples from each writer in the closed-set. A writer profile is also estimated from the questioned document. The statistical model compares the writer profile from the questioned document with each of the writer profiles from the closed-set of potential writers and estimates the posterior probability that each closed-set writer wrote the questioned document. 
+Handwriter is designed to assist forensic examiners by analyzing handwritten documents against a *closed set* of potential writers. It determines the probability that each writer wrote the document. Whether you are a forensic document examiner, legal professional, academic, or simply curious about how statistics are applied to handwriting, handwriter provides an automated way to evaluate handwriting samples.
+
+## Quick Start
+
+### VIEW A DEMO
+
+View a demo of handwriter on handwritten documents from the CSAFE Handwriting Database. Go to [demo](https://csafe.shinyapps.io/handwriterAppDemo/).
+
+### SIMULATE CASEWORK WITH EXAMPLE DOCUMENTS
+
+#### INSTALLATION
+
+Handwriter requires R, RStudio IDE, and JAGS.
+
+-   Install R and RStudio from [POSIT](https://posit.co/download/rstudio-desktop/)
+-   Install JAGS from [SourceForge](https://sourceforge.net/projects/mcmc-jags/files/)
+
+#### LAUNCH THE APP
+
+Open RStudio, navigate to the console window, and type:
+
+```{r, eval = FALSE}
+install.packages("devtools")
+devtools::install_github("CSAFE-ISU/handwriterApp")
+library(handwriterApp)
+handwriterApp()
+```
+
+In the pop-up window, click **Open in Browser**. If you use the app in the pop-up window
+instead of in a browser, some links will not work.
+
+Click **Simulate Casework** and follow the instructions in the app.
 
-## Installation
+## Advanced
 You can install handwriter from CRAN with:
 ``` r
 install.packages("handwriter")

_quarto/.gitignore

@@ -0,0 +1 @@
+/.quarto/

docs/CITATION.md → _quarto/CITATION.md

@@ -3,11 +3,10 @@
 ```verbatim
 To cite package ‘handwriter’ in publications use:
 
-  Iowa State University of Science and Technology on behalf of its
-  Center for Statistics and Applications in Forensic Evidence, Berry
-  N, Reinders S, Taylor J (2024). _handwriter: Handwriting Analysis in
-  R_. R package version 3.1.1.9000, commit
-  2ca3187a3e750fed34d373eae7dd587483c96b75,
+  Iowa State University of Science and Technology on behalf of its Center for
+  Statistics and Applications in Forensic Evidence, Berry N, Reinders S, Taylor
+  J (2024). _handwriter: Handwriting Analysis in R_. R package version
+  3.1.1.9000, commit 3b29e861c4bcaed6062f79ebb75c000f9bd86413,
   <https://github.com/CSAFE-ISU/handwriter>.
 
 A BibTeX entry for LaTeX users is
@@ -16,7 +15,7 @@ A BibTeX entry for LaTeX users is
     title = {handwriter: Handwriting Analysis in R},
     author = {{Iowa State University of Science and Technology on behalf of its Center for Statistics and Applications in Forensic Evidence} and Nick Berry and Stephanie Reinders and James Taylor},
     year = {2024},
-    note = {R package version 3.1.1.9000, commit 2ca3187a3e750fed34d373eae7dd587483c96b75},
+    note = {R package version 3.1.1.9000, commit 3b29e861c4bcaed6062f79ebb75c000f9bd86413},
     url = {https://github.com/CSAFE-ISU/handwriter},
   }
 ```

docs/NEWS.md → _quarto/NEWS.md

@@ -15,6 +15,8 @@
 * Fixed bug in `format_template_data()` where the function coerced writer IDs to integers even
 if the writer IDs contained characters.
 
+* Fixed bug in `get_clusters_batch()` where the function would stall but not return an error message if a document had a graph with a large number of edges (paths). Now the function deletes graphs with more than 30 edges. 
+
 # handwriter 3.1.1
 
 ## Patches

_quarto/_quarto.yml

@@ -0,0 +1,117 @@
+project:
+  type: website
+website:
+  title: handwriter
+  navbar:
+    search: true
+    right:
+      - icon: github
+        href: https://github.com/CSAFE-ISU/handwriter
+        aria-label: handwriter GitHub
+  sidebar:
+    collapse-level: 1
+    contents:
+      - text: Home
+        file: index.qmd
+      - section: Articles
+        contents:
+          - vignettes/handwriter.Rmd
+      - section: Reference
+        contents:
+          - text: about_variable
+            file: man/about_variable.qmd
+          - text: addToFeatures
+            file: man/addToFeatures.qmd
+          - text: analyze_questioned_documents
+            file: man/analyze_questioned_documents.qmd
+          - text: calculate_accuracy
+            file: man/calculate_accuracy.qmd
+          - text: cleanBinaryImage
+            file: man/cleanBinaryImage.qmd
+          - text: csafe
+            file: man/csafe.qmd
+          - text: drop_burnin
+            file: man/drop_burnin.qmd
+          - text: example_analysis
+            file: man/example_analysis.qmd
+          - text: example_cluster_template
+            file: man/example_cluster_template.qmd
+          - text: example_model
+            file: man/example_model.qmd
+          - text: extractGraphs
+            file: man/extractGraphs.qmd
+          - text: fit_model
+            file: man/fit_model.qmd
+          - text: format_template_data
+            file: man/format_template_data.qmd
+          - text: get_cluster_fill_counts
+            file: man/get_cluster_fill_counts.qmd
+          - text: get_clusters_batch
+            file: man/get_clusters_batch.qmd
+          - text: get_credible_intervals
+            file: man/get_credible_intervals.qmd
+          - text: get_posterior_probabilities
+            file: man/get_posterior_probabilities.qmd
+          - text: graphToPrototype
+            file: man/graphToPrototype.qmd
+          - text: london
+            file: man/london.qmd
+          - text: make_clustering_template
+            file: man/make_clustering_template.qmd
+          - text: message
+            file: man/message.qmd
+          - text: nature1
+            file: man/nature1.qmd
+          - text: plot_cluster_centers
+            file: man/plot_cluster_centers.qmd
+          - text: plot_cluster_fill_counts
+            file: man/plot_cluster_fill_counts.qmd
+          - text: plot_cluster_fill_rates
+            file: man/plot_cluster_fill_rates.qmd
+          - text: plot_credible_intervals
+            file: man/plot_credible_intervals.qmd
+          - text: plot_posterior_probabilities
+            file: man/plot_posterior_probabilities.qmd
+          - text: plot_trace
+            file: man/plot_trace.qmd
+          - text: plotImage
+            file: man/plotImage.qmd
+          - text: plotImageThinned
+            file: man/plotImageThinned.qmd
+          - text: plotLetter
+            file: man/plotLetter.qmd
+          - text: plotLine
+            file: man/plotLine.qmd
+          - text: plotNodes
+            file: man/plotNodes.qmd
+          - text: process_batch_dir
+            file: man/process_batch_dir.qmd
+          - text: process_batch_list
+            file: man/process_batch_list.qmd
+          - text: processDocument
+            file: man/processDocument.qmd
+          - text: processHandwriting
+            file: man/processHandwriting.qmd
+          - text: read_and_process
+            file: man/read_and_process.qmd
+          - text: readPNGBinary
+            file: man/readPNGBinary.qmd
+          - text: rgb2grayscale
+            file: man/rgb2grayscale.qmd
+          - text: rgba2rgb
+            file: man/rgba2rgb.qmd
+          - text: thinImage
+            file: man/thinImage.qmd
+          - text: twoSent
+            file: man/twoSent.qmd
+          - text: whichToFill
+            file: man/whichToFill.qmd
+      - text: News
+        file: NEWS.md
+      - text: License
+        file: LICENSE.md
+      - text: Citation
+        file: CITATION.md
+format:
+  html:
+    css: styles.css